Masaru Tomita

Publication Activity (10 Years)

Years Active: 1984-2022
Publications (10 Years): 6

Top Venues

CinC

BMC Bioinform.

ICONIP (1)

Source Code Biol. Medicine

Publications

Rira Matsuta, Hiroyuki Yamamoto, Masaru Tomita, Rintaro Saito
iDMET: network-based approach for integrating differential analysis of cancer metabolomics. BMC Bioinform. 23 (1) (2022)
Yusuke Kobayashi, Liuyang Song, Masaru Tomita, Peng Chen
Automatic Fault Detection and Isolation Method for Roller Bearing Using Hybrid-GA and Sequential Fuzzy Inference. Sensors 19 (16) (2019)
Hitoshi Iuchi, Masahiro Sugimoto, Masaru Tomita
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data. BMC Bioinform. 19 (1) (2018)
Maiko Wakita, Hitomi Sano, Yasuhiro Naito, Masaru Tomita
Combination of Quantitative Changes in Ionic Components to Enhance the Contractile Force during T-tubule Development. CinC (2016)
Kotone Itaya, Koichi Takahashi, Masayoshi Nakamura, Moriyoshi Koizumi, Naoya Arakawa, Masaru Tomita, Hiroshi Yamakawa
BriCA: A Modular Software Platform for Whole Brain Architecture. ICONIP (1) (2016)
Hitomi Sano, Yasuhiro Naito, Masaru Tomita
Simulation Study on the Balance of Glycolytic ATP Production and Oxidative Phosphorylation in Embryonic and Adult Ventricular Cells. CinC (2016)
Hanae Shimo, Satya Nanda Vel Arjunan, Hiroaki Machiyama, Taiko Nishino, Makoto Suematsu, Hideaki Fujita, Masaru Tomita, Koichi Takahashi
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS Comput. Biol. 11 (6) (2015)
Hitomi Sano, Yuichiro Tanaka, Yasuhiro Naito, Masaru Tomita
Sensitivity Analysis of Ectopic Electrical Activity in Pulmonary Vein Myocardium. CinC (2015)
Mao Takiguchi, Tamami Toki, Hitomi Sano, Yasuhiro Naito, Masaru Tomita
Modeling and Simulation of Developmental Changes in Contractile Apparatus of Ventricular Cells. CinC (2015)
Koichi Takahashi, Kotone Itaya, Masayoshi Nakamura, Moriyoshi Koizumi, Naoya Arakawa, Masaru Tomita, Hiroshi Yamakawa
A Generic Software Platform for Brain-inspired Cognitive Computing. BICA (2015)
Hitomi Sano, Tamami Toki, Yasuhiro Naito, Masaru Tomita
Contribution of Developmental Changes in Energy Metabolism to Excitation-Contraction Coupling of a Ventricular Cell: A Simulation Study. CinC (2014)
Kazuki Oshita, Masaru Tomita, Kazuharu Arakawa
G-Links: a gene-centric link acquisition service. F1000Research 3 (2014)
Hidetoshi Itaya, Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses. Source Code Biol. Medicine 8 (2013)
Cornelia Amariei, Rainer Machné, Kalesh Sasidharan, Willi Gottstein, Masaru Tomita, Tomoyoshi Soga, David Lloyd, Douglas B. Murray
The dynamics of cellular energetics during continuous yeast culture. EMBC (2013)
Masahiro Takada, Masahiro Sugimoto, Yasuhiro Naito, Hyeong-Gon Moon, Wonshik Han, Dong-Young Noh, Masahide Kondo, Katsumasa Kuroi, Hironobu Sasano, Takashi Inamoto, Masaru Tomita, Masakazu Toi
Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model. BMC Medical Informatics Decis. Mak. 12 (2012)
Masahiro Sugimoto, Satsuki Ikeda, Kanako Niigata, Masaru Tomita, Hideyo Sato, Tomoyoshi Soga
MMMDB: Mouse Multiple Tissue Metabolome Database. Nucleic Acids Res. 40 (Database-Issue) (2012)
Nozomu Yachie, Rintaro Saito, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama
Integrative Features of the Yeast Phosphoproteome and Protein-Protein Interaction Map. PLoS Comput. Biol. 7 (1) (2011)
Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
KBWS: an EMBOSS associated package for accessing bioinformatics web services. Source Code Biol. Medicine 6 (2011)
Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. BMC Bioinform. 11 (2010)
Kazuharu Arakawa, Nobuhiro Kido, Kazuki Oshita, Masaru Tomita
G-language genome analysis environment with REST and SOAP web service interfaces. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, Masaru Tomita
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinform. 11 (2010)
Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama
emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinform. 26 (4) (2010)
Haruo Suzuki, Rintaro Saito, Masaru Tomita
Measure of synonymous codon usage diversity among genes in bacteria. BMC Bioinform. 10 (2009)
Kumar Selvarajoo, Masaru Tomita, Masa Tsuchiya
Can Complex Cellular Processes be Governed by Simple Linear Rules? J. Bioinform. Comput. Biol. 7 (1) (2009)
Kazuharu Arakawa, Kazuki Oshita, Masaru Tomita
A web server for interactive and zoomable Chaos Game Representation images. Source Code Biol. Medicine 4 (2009)
Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita
Genome Projector: zoomable genome map with multiple views. BMC Bioinform. 10 (2009)
Ryoji Yanashima, Noriyuki Kitagawa, Yoshiya Matsubara, Robert Weatheritt, Kotaro Oka, Shinichi Kikuchi, Masaru Tomita, Shun Ishizaki
Network features and pathway analyses of a signal transduction cascade. Frontiers Neuroinformatics 3 (2009)
Hiroshi Ohno, Yasuhiro Naito, Hiromu Nakajima, Masaru Tomita
Construction of a Biological Tissue Model Based on a Single-Cell Model: A Computer Simulation of Metabolic Heterogeneity in the Liver Lobule. Artif. Life 14 (1) (2008)
Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Kotaro Oka, Masaru Tomita
Algebraic Method for the Analysis of Signaling Crosstalk. Artif. Life 14 (1) (2008)
Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. Bioinform. 24 (14) (2008)
Anton Kratz, Masaru Tomita, Arun Krishnan
GeNESiS: gene network evolution simulation software. BMC Bioinform. 9 (2008)
Yukino Ogawa, Kazuharu Arakawa, Kazunari Kaizu, Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita
. Artif. Life 14 (1) (2008)
Kyota Ishii, Seira Nakamura, Mineo Morohashi, Masahiro Sugimoto, Yoshiaki Ohashi, Shinichi Kikuchi, Masaru Tomita
Comparison of metabolite production capability indices generated by network analysis methods. Biosyst. 91 (1) (2008)
Shigeru Sato, Masanori Arita, Tomoyoshi Soga, Takaaki Nishioka, Masaru Tomita
Time-resolved metabolomics reveals metabolic modulation in rice foliage. BMC Syst. Biol. 2 (2008)
Yoshiteru Negishi, Hiroyuki Nakamura, Nozomu Yachie, Rintaro Saito, Masaru Tomita
eXpanda: An Integrated Platform for Network Analysis and Visualization. Silico Biol. 7 (2) (2007)
Haruo Suzuki, Rintaro Saito, Masaru Tomita
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria. EURASIP J. Bioinform. Syst. Biol. 2007 (2007)
Yuri Matsuzaki, Shinichi Kikuchi, Masaru Tomita
Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis. Artif. Intell. Medicine 41 (2) (2007)
Satoshi Tamaki, Kazuharu Arakawa, Nobuaki Kono, Masaru Tomita
Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics. Genom. Proteom. Bioinform. 5 (1) (2007)
Koya Mori, Rintaro Saito, Shinichi Kikuchi, Masaru Tomita
Inferring rules of Escherichia coli translational efficiency using an artificial neural network. Biosyst. 90 (2) (2007)
Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga, Masaru Tomita
Visualization of three-way comparisons of omics data. BMC Bioinform. 8 (2007)
Hiroyuki Fujita, Katsuya Fukuda, Koichiro Sawa, Masaru Tomita, Masato Murakami, Naomichi Sakai, Izumi Hirabayashi
Consideration on Contact Mechanism of YBaCuO Bulk Superconductor with Deposited Metal Layer. IEICE Trans. Electron. (7) (2007)
Richard Baran, Hayataro Kochi, Natsumi Saito, Makoto Suematsu, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita
MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinform. 7 (2006)
Gek Huey Chua, Arun Krishnan, Kuo-Bin Li, Masaru Tomita
Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins. J. Bioinform. Comput. Biol. 4 (6) (2006)
Kazuharu Arakawa, Yoichi Nakayama, Masaru Tomita
GPAC: Benchmarking the Sensitivity of Genome Informatics Analysis to Genome Annotation Completeness. Silico Biol. 6 (1-2) (2006)
Junichi Sugahara, Nozomu Yachie, Yasuhiko Sekine, Akiko Soma, Motomu Matsui, Masaru Tomita, Akio Kanai
SPLITS: A New Program for Predicting Split and Intron-Containing tRNA Genes at the Genome Level. Silico Biol. 6 (5) (2006)
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinform. 7 (2006)
Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita
MEGU: Pathway Mapping Web-Service Based on KEGG and SVG. Silico Biol. 6 (6) (2006)
Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita
Parameter estimation for stiff equations of biosystems using radial basis function networks. BMC Bioinform. 7 (2006)
Gabor Bereczki, Masaru Tomita
An interaction knowledgebase for biomolecular modeling. ICDM (Workshops) (2006)
Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, Masaru Tomita
HybGFS: a hybrid method for genome-fingerprint scanning. BMC Bioinform. 7 (2006)
Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. BMC Bioinform. 6 (2005)
Kazuharu Arakawa, Nobuaki Kono, Yohei Yamada, Hirotada Mori, Masaru Tomita
KEGG-Based Pathway Visualization Tool for Complex Omics Data. Silico Biol. 5 (4) (2005)
Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinform. 21 (9) (2005)
Sumie Kitamura-Abe, Hitomi Itoh, Takanori Washio, Akihiro Tsutsumi, Masaru Tomita
Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas. J. Bioinform. Comput. Biol. 2 (2) (2004)
Yasushi Kiyoki, Masa Inakage, Masahiko Satoh, Masaru Tomita
Future Directions for Cyber Knowledge and Databases. SAINT Workshops (2004)
Katsuyuki Yugi, Masaru Tomita
A general computational model of mitochondrial metabolism in a whole organelle scale. Bioinform. 20 (11) (2004)
Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita
A multi-algorithm, multi-timescale method for cell simulation. Bioinform. 20 (4) (2004)
Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita
Distributed Cell Biology Simulations with E-Cell System. LSGRID (2004)
Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita
Computational Analysis of Stop Codon Readthrough in D.melanogaster. Bioinform. 19 (11) (2003)
Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, D. Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19 (4) (2003)
Koichi Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, Fumihiko Miyoshi, Yasuhiro Naito, Yoichi Nakayama, Masaru Tomita
E-Cell 2: Multi-platform E-Cell simulation system. Bioinform. 19 (13) (2003)
Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita
Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinform. 19 (5) (2003)
Shinichi Kikuchi, Kenji Fujimoto, Noriyuki Kitagawa, Taro Fuchikawa, Michiko Abe, Kotaro Oka, Kohtaro Takei, Masaru Tomita
Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A. Neural Networks 16 (9) (2003)
Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinform. 19 (2) (2003)
Masaru Tomita
Toward Computer Simulation of the Whole Cell. Gene Regulations and Metabolism (2002)
Kenta Hashimoto, Sae Seno, Pawan Kumar Dhar, Masaru Tomita
Integrative modeling of gene expression and metabolism with E-CELL System. Artif. Life Robotics 6 (3) (2002)
Kouichi Takahashi, Katsuyuki Yugi, Kenta Hashimoto, Yohei Yamada, Christopher J. F. Pickett, Masaru Tomita
Computational Challenges in Cell Simulation: A Software Engineering Approach. IEEE Intell. Syst. 17 (5) (2002)
Masaru Tomita
Towards Computer Aided Design (CAD) of Useful Microorganisms. Bioinform. 17 (12) (2001)
Masaru Tomita
E-CELL Project: Towards Whole Cell Simulation. German Conference on Bioinformatics (2001)
Ryuta Fukuda, Junko Hara, William Rodman Shankle, Masaru Tomita
Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex. Neurocomputing (2000)
Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Yusuke Saito, Tom Shimizu, Yoichi Nakayama
The E-CELL project: towards integrative simulation of cellular processes. RECOMB (2000)
Y. Osada, Rintaro Saito, Masaru Tomita
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes. Bioinform. 15 (7) (1999)
Ryuta Fukuda, Junko Hara, William Rodman Shankle, Toshio Inui, Masaru Tomita
Predicting human cortical connectivity for language areas using the Conel database. IJCNN (1999)
Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Thomas Simon Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig Venter, Clyde A. Hutchison III
E-CELL: software environment for whole-cell simulation. Bioinform. 15 (1) (1999)
Masaru Tomita, Takashi Kido
Sacrificial Acts in Single Round Prisoner's Dilemma. Informatica (Slovenia) 18 (4) (1994)
Monika Woszczyna, Naomi Aoki-Waibel, Finn Dag Buø, Noah Coccaro, Keiko Horiguchi, Thomas Kemp, Alon Lavie, Arthur E. McNair, Thomas Polzin, Ivica Rogina, Carolyn Penstein Rosé, Tanja Schultz, Bernhard Suhm, Masaru Tomita, Alex Waibel
JANUS 93: towards spontaneous speech translation. ICASSP (1) (1994)
Monika Woszczyna, Noah Coccaro, Andreas Eisele, Alon Lavie, Arthur E. McNair, Thomas Polzin, Ivica Rogina, Carolyn Penstein Rosé, Tilo Sloboda, Masaru Tomita, J. Tsutsumi, Naomi Aoki-Waibel, Alex Waibel, Wayne H. Ward
Recent advances in JANUS: a speech translation system. HLT (1993)
Monika Woszczyna, Noah Coccaro, Andreas Eisele, Alon Lavie, Arthur E. McNair, Thomas Polzin, Ivica Rogina, Carolyn Penstein Rosé, Tilo Sloboda, Masaru Tomita, J. Tsutsumi, Naomi Aoki-Waibel, Alex Waibel, Wayne H. Ward
Recent advances in JANUS: a speech translation system. EUROSPEECH (1993)
Gennaro Costagliola, Shi-Kuo Chang, Masaru Tomita
Parsing 2D Languages by a Pictorial GLR Parser. Advanced Visual Interfaces (1992)
Gennaro Costagliola, Masaru Tomita, Shi-Kuo Chang
A Generalized Parser for 2-D Languages. VL (1991)
Masaru Tomita
The Generalized LR Parser/Compiler V8-4: A Software Package for Practical NL Projects. COLING (1990)
Hiroaki Kitano, Tetsuya Higuchi, Masaru Tomita
Massively parallel spoken language processing using a parallel associative processor IXM2. ICSLP (1990)
Masaru Tomita
Parsing 2-Dimensional Language. IWPT (1989)
Hiroaki Kitano, Teruko Mitamura, Masaru Tomita
Massively Parallel Parsing in ΦDmDialog: Integrated Architecture for Parsing Speech Inputs. IWPT (1989)
Hiroaki Saito, Masaru Tomita
Parsing noisy sentences. COLING (1988)
Masaru Tomita
Combining lexicon-driven parsing and phrase-structure-based parsing. COLING (1988)
Masaru Tomita
"Linguistic" sentences and "real" sentences. COLING (1988)
Hideto Tomabechi, Teruko Mitamura, Masaru Tomita
Direct Memory Access Translation for Speech Input. FGCS (1988)
Hideto Tomabechi, Masaru Tomita
Application of the direct memory access paradigm to NL interfaces to knowledge-based systems. COLING (1988)
Masaru Tomita
Graph-Structured Stack and Natural Language Parsing. ACL (1988)
Hideto Tomabechi, Masaru Tomita
The Integration of Unification-Based Syntax/Semantics and Memory-Based Pragmatics for Real-Time Understanding of Noisy Continuous Speech Input. AAAI (1988)
Masaru Tomita
An Efficient Augmented-Context-Free Parsing Algorithm. Comput. Linguistics 13 (1-2) (1987)
Masaru Tomita, Jaime G. Carbonell
The Universal Parser Architecture for Knowledge-based Machine Translation. IJCAI (1987)
Masaru Tomita
An efficient word lattice parsing algorithm for continuous speech recognition. ICASSP (1986)
Philip J. Hayes, Alexander G. Hauptmann, Jaime G. Carbonell, Masaru Tomita
Parsing Spoken Language: A Semantic Caseframe Approach. COLING (1986)
Masaru Tomita, Jaime G. Carbonell
Another Stride Towards Knowledge-Based Machine Translation. COLING (1986)
Masaru Tomita
Sentence disambiguation by asking. Mach. Transl. 1 (1) (1986)
Sei-ichi Nakagawa, Alexander G. Hauptmann, Masaru Tomita
On quick word spotting techniques. ICASSP (1986)
Masaru Tomita
An Efficient Context-Free Parsing Algorithm for Natural Languages. IJCAI (1985)
Masaru Tomita
LR Parsers For Natural Languages. COLING (1984)

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Publication Activity (10 Years)

Top Topics

Top Venues

Masaru Tomita